[gmx-users] Possible bug in g_hbond with implicit solvent

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 19 17:45:26 CEST 2011

Mark Abraham wrote:
> On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:
>> Hi All,
>> I wanted to solicit some feedback on what I think may be a bug related 
>> to periodicity handling and/or implicit solvent simulations.  I ran 
>> some simulations of a few model peptides (some helices, hairpins, etc) 
>> and I got what I believed to be very inflated results for backbone 
>> hydrogen bonds.  For instance, a helical peptide with only 17 residues 
>> had, on average, 23.5 hydrogen bonds within the backbone alone, which, 
>> judging from the configurations, couldn't really be possible.
> Does the structure file input to g_hbond have a spuriously small box?

It does, and I suspect this is where the problem ultimately lies.  For the 
simulation, with "pbc = no" the box vectors get ignored and everything is fine. 
  For analysis, however, it seems that the PBC routines are still trying to fit 
everything into that tiny box and thus basically all possible H-bonds are 
detected as being present because the distances are so small.

Re-generating the .tpr file with a new, larger, box does not fix the problem, 
likely because the .xtc still has the tiny box.  Manipulating the trajectory 
with trjconv -box -center seems to work, though.  So I suppose this is an 
acceptable workaround, though it still may be a problem worth looking into.

Thanks for the inspiration; hadn't thought about trying to change the box after 
the fact :)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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